Table 2. .
PCoA Significance Tests[Note]
| All SNPs(n=9,111) |
SNPs >50 kb Apart(n=6,349) |
SNPs >100 kb Apart(n=5,555) |
||||
| Test | Adjusteda r2 (P) | SKT Pb | Adjusteda r2 (P) | SKT Pb | Adjusteda r2 (P) | SKT Pb |
| PC1 | .90 (<.001) | <.0001 | .89 (<.001) | <.0001 | .90 (<.001) | <.0001 |
| PC2 | .78 (<.001) | <.0001 | .74 (<.001) | <.0001 | .72 (<.001) | <.0001 |
| PC3 | .43 (<.001) | <.0001 | .50 (<.001) | <.0001 | .35 (<.001) | <.0001 |
| PC4 | .54 (<.001) | <.0001 | .30 (<.001) | <.0001 | .19 (<.01) | <.01 |
| PC5 | <.1 (NS) | NS | <.1 (NS) | NS | .13 (<.05) | <.001 |
| PC6 | <.1 (NS) | NS | <.1 (NS) | NS | .18 (<.01) | <.001 |
| PC7 | <.1 (NS) | NS | .17 (<.01) | NS | .18 (<.01) | <.01 |
| PC8 | <.1 (NS) | NS | <.1 (NS) | NS | <.1 (NS) | NS |
| PC9 | <.1 (NS) | <.01 | <.1 (NS) | NS | <.1 (NS) | NS |
| PC10 | .13 (<.05) | NS | <.1 (NS) | NS | <.1 (NS) | NS |
Note.— Significance tests using the ANOVA and SKT. PCoA was conducted separately for each SNP set. The French singleton and the German outlier were excluded. Percentages of the variance explained by each PC are generally the same in all three cases (fig. 4A). NS = not significant at the .05 level.
a
ANOVA correlation coefficient (adjusted r2) in bold.
b
Combined P value calculated for SKT, as described in the text.